Mercurial > repos > computational-metabolomics > mspurity_averagefragspectra

annotate purityA.R @ 1:4207233ead9c draft

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"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
author computational-metabolomics
date Thu, 05 Dec 2019 07:37:41 -0500
parents 50eedf5ad217
children 52d48bcd3608
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
parents:
diff changeset
1 library(msPurity)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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2 library(optparse)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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3 print(sessionInfo())
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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4
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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5 option_list <- list(
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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6 make_option(c("-o", "--out_dir"), type="character"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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7 make_option("--mzML_files", type="character"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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8 make_option("--galaxy_names", type="character"),
1
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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9 make_option("--minOffset", type="numeric"),
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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10 make_option("--maxOffset", type="numeric"),
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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11 make_option("--ilim", type="numeric"),
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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12 make_option("--iwNorm", default="none", type="character"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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13 make_option("--exclude_isotopes", action="store_true"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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14 make_option("--isotope_matrix", type="character"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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15 make_option("--mostIntense", action="store_true"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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16 make_option("--plotP", action="store_true"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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17 make_option("--nearest", action="store_true"),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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18 make_option("--cores", default=4),
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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19 make_option("--ppmInterp", default=7)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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20 )
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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22 opt <- parse_args(OptionParser(option_list=option_list))
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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23 print(opt)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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26 if (opt$iwNorm=='none'){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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27 iwNorm = FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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28 iwNormFun = NULL
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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29 }else if (opt$iwNorm=='gauss'){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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30 iwNorm = TRUE
1
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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31 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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32 print('User has to define offsets if using Gaussian normalisation')
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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33 }else{
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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34 iwNormFun = msPurity::iwNormGauss(minOff=-as.numeric(opt$minOffset),
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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35 maxOff=as.numeric(opt$maxOffset))
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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36 }
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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37 }else if (opt$iwNorm=='rcosine'){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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38 iwNorm = TRUE
1
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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39 if (is.null(opt$minOffset) || is.null(opt$maxOffset)){
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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40 print('User has to define offsets if using R-cosine normalisation')
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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41 }else{
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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42 iwNormFun = msPurity::iwNormRcosine(minOff=-as.numeric(opt$minOffset),
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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43 maxOff=as.numeric(opt$maxOffset))
4207233ead9c "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20d432cdc6326114d05c26fd51889b872513b57d"
computational-metabolomics
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44 }
0
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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45 }else if (opt$iwNorm=='QE5'){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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46 iwNorm = TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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47 iwNormFun = msPurity::iwNormQE.5()
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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48 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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49
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50 filepaths <- trimws(strsplit(opt$mzML_files, ',')[[1]])
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
computational-metabolomics
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51 filepaths <- filepaths[filepaths != ""]
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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52
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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53
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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54
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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55 if(is.null(opt$minOffset) || is.null(opt$maxOffset)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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56 offsets = NA
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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57 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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58 offsets = as.numeric(c(opt$minOffset, opt$maxOffset))
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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59 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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61
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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62 if(is.null(opt$mostIntense)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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63 mostIntense = FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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64 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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65 mostIntense = TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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66 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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67
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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68 if(is.null(opt$nearest)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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69 nearest = FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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70 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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71 nearest = TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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72 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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73
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74 if(is.null(opt$plotP)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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75 plotP = FALSE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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76 plotdir = NULL
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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77 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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78 plotP = TRUE
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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79 plotdir = opt$out_dir
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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80 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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81
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82
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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83 if (is.null(opt$isotope_matrix)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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84 im <- NULL
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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85 }else{
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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86 im <- read.table(opt$isotope_matrix,
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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87 header = TRUE, sep='\t', stringsAsFactors = FALSE)
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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88 }
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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89
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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90 if (is.null(opt$exclude_isotopes)){
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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91 isotopes <- FALSE
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92 }else{
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93 isotopes <- TRUE
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94 }
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95
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96 pa <- msPurity::purityA(filepaths,
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97 cores = opt$cores,
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98 mostIntense = mostIntense,
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99 nearest = nearest,
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100 offsets = offsets,
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101 plotP = plotP,
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102 plotdir = plotdir,
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103 interpol = "linear",
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104 iwNorm = iwNorm,
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105 iwNormFun = iwNormFun,
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106 ilim = opt$ilim,
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107 mzRback = "pwiz",
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108 isotopes = isotopes,
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109 im = im,
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110 ppmInterp = opt$ppmInterp)
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111
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112
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113 if (!is.null(opt$galaxy_names)){
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114 galaxy_names <- trimws(strsplit(opt$galaxy_names, ',')[[1]])
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115 galaxy_names <- galaxy_names[galaxy_names != ""]
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116 names(pa@fileList) <- galaxy_names
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117 }
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118
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119 print(pa)
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120 save(pa, file=file.path(opt$out_dir, 'purityA_output.RData'))
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121
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122 pa@puritydf$filename <- sapply(pa@puritydf$fileid, function(x) names(pa@fileList)[as.integer(x)])
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123
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124 print(head(pa@puritydf))
50eedf5ad217 "planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
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125 write.table(pa@puritydf, file.path(opt$out_dir, 'purityA_output.tsv'), row.names=FALSE, sep='\t')
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126
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127 # removed_peaks <- data.frame(removed_peaks)
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128 # write.table(data.frame('ID'=rownames(removed_peaks),removed_peaks),
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129 # file.path(opt$out_dir, 'removed_peaks.txt'), row.names=FALSE, sep='\t')